"It is ancient, a relic that survived the destruction of Malachor. It was always here, far before the Mandalorian Wars. It draws death and hate to it, channels it. Atrocities feed its power, and with its power, it creates hunger. Many Jedi have been consumed by it."

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"It has been here for thousands of years. It is a place where Sith teachings run strong… It is the threshold of the borders of an ancient empire. Kreia says that it was a place of reflection for the ancient Sith… a gateway to their lands. It drew Lord Revan… and it calls to her as well. She said that the teachings here will lead one to the Sith… the true Sith… and all their shadowed worlds. This place led Revan to the graveyards of Korriban… and beyond."

The Trayus Academy was a training center built millennia before the Mandalorian Wars by the ancient Sith; and it would become the source of Malachor V's dark side energies. Eventually the Academy as well as the planet was abandoned by the Sith and was left unvisited for centuries.

During the Mandalorian Wars in the year 3961 BBY, a young Jedi Knight named Revan rediscovered Malachor while scouting for bases along the Outer Rim when he heard stories of a world the Mandalorians were forbidden to step foot on according to their culture. Wishing to discover why Malachor V was a taboo world to the Mandalorians, Revan secretly investigated the planet, unaware he was about to discover far more than what he was looking for.

Revan quickly unearthed the remains of entire cities buried beneath the surface. Amidst the ruins, he came across the Trayus Academy and within he found countless records of Sith knowledge and history. Revan rediscovered the location of the planet Korriban, and uncovered evidence that the ancient Sith continued to exist beyond the boundaries of known space and continued to pose a threat to the galaxy.

Coming to the conclusion that the Galactic Republic, as it stood, was ill-equipped to defend the galaxy from the return of the ancient Sith, Revan believed that a new government needed to rise in its place, a military force that was capable of repelling such a powerful threat and lead by one who understood them. Unbeknownst to even his closest confidants such as Malak, Revan constructed a stronghold and used Malachor's dark side energies to bind the most trusted of his followers to his will. The Sith assassin order was founded as a result.

Returning to the war, Revan led the Republic to victory over the Mandalorians. One year after rediscovering the Trayus Academy, Revan forced a final confrontation with the Mandalorians above Malachor V. In utter secrecy, he had prepared a superweapon, known as the "Mass Shadow Generator," which was to be the centerpiece of a trap with which he hoped to bring about a conclusive end to the Mandalorian Wars. Overseeing the device's use was a trusted Jedi General, Meetra Surik (the future Jedi Exile).

Revan lured the Mandalorians to Malachor, and as the fighting grew intense, on his order, Surik, one of his most trusted generals activated the generators. In the resulting cataclysm, a significant portion of both the Mandalorian and Republic fleets were drawn from orbit into a vast gravity vortex that was powerful enough to crush the countless ships into the planet's crust and fracture the world to its core. Remarkably, the Trayus Academy survived the catastrophic event intact.

Following his victory and affected by the knowledge gained at Trayus Academy, Revan traveled with Malak to the Unknown Regions. There on Dromund Kaas he encountered the Sith Emperor and was subdued to the Emperor's will, and he was inducted into the Sith, adding the Darth title to his name, becoming Darth Revan. The Emperor then ordered him to search for the Star Forge for the Emperor, planning on using the Star Forge to speed up the building of the Imperial armada. During the search, Darth Revan decided to rebel against the Sith Emperor and declared himself Dark Lord of the Sith and founded his own Sith Empire. During the Jedi Civil War, circa 3959–3956 BBY, he used the Trayus Academy as one of several secret Sith bases dedicated to the conversion of captured Jedi. Throughout the war, Jedi were captured by his Sith assassins, and other specially trained forces, and brought to the Academy. The corruptive nature of the location weakened their wills so that Revan and his loyal servants could easily lure them to the dark side. In such places, he converted hosts of Jedi into loyal Dark Jedi and Sith assassins for his empire.

A year after the Sith were defeated by the Galactic Republic during the Jedi Civil War, a redeemed Revan departed for the Unknown Regions in a solitary quest to defeat the "True Sith." Meanwhile, Revan's former Jedi Master, a Jedi named Kreia, feared that her teachings had led Revan to the dark side and went in search of her pupil—a search that would eventually lead her to Malachor V. Kreia walked upon the surface of the planet and was overcome. She fell to the dark side and become Darth Traya. In time, she would study the planet's secrets and rise to command the Trayus Academy and the Sith Assassins which still lingered there. Darth Traya reestablished the Academy to train, convert, and create a new generation of Sith whose sole mission was to destroy the Jedi Order.

Darth Traya soon discovered two Sith Lords who shared her vision. Darth Nihilus and Darth Sion joined her cause and together they formed a Sith Triumvirate. Under the leadership of the three Sith Lords, the Trayus Academy reached its zenith. Based within their hidden Academy on Malachor V, the Sith Lords commanded legions of Assassins who hunted the remaining Jedi to the very brink of extinction. Darth Traya had managed to unite the fragmented Sith forces and lead them to victory once more, but her success would not save her. In a sudden act of betrayal, her two apprentices joined forces, stripped her of power, and exiled her.

In 3951 BBY, Kreia located Meetra Surik who was the only Jedi who had fought with Revan against the Mandalorians at Malachor V and yet remained uncorrupted. Plotting revenge against her apprentices, Kreia orchestrated events to set up a final confrontation between herself and Surik at the Trayus Academy. After slaying Darth Nihilus, Surik arrived at the Academy to combat the Sith lurking there. She invaded the academy and eliminated every Sith minion that crossed her path. Moments after defeating Darth Sion and Traya in a series of lightsaber duels, Malachor V and the Trayus Academy on its surface were utterly destroyed when the Mass Shadow Generator was reactivated on Surik's orders.

The entrance of the Trayus Academy from the Malachor Depths opened onto an antechamber that connected to the eastern and western halls of the complex. The Trayus Crescent, located to the west, was a hall with many alcoves that were frequented by Sith commandos. To the east, the Trayus Proving Grounds was a warren of small and cramped rooms in which many Dark Jedi and Sith commandos could be found. The northern point of both wings led to the Academy's central area, the last bit of open space before the innermost sanctum of the Trayus Academy was known as the Trayus Core.